Welcome to JustAnswer, I'm here to help get your problem resolved. Please feel free to ask follow up questions, it is part of the process.
Here are the instructions for that part of the job. There is no sequence for either the upper or lower but I included this info and torque in case it would help.
2. Place a drop (approximately 1/4 in. diameter) of Mopar Engine RTV GEN II onto each of the four manifold to cylinder head gasket corners.
3. Carefully install the new intake manifold gasket. Torque end seal retainer screws to 12 Nm (105 in. lbs.).
4. Install intake manifold and bolts and torque to 1 Nm (10 in. lbs.). Then torque bolts to 22 Nm (200 in. lbs.) in sequence shown in (Fig. 50). Then torque again to 22 Nm (200 in. lbs.). After intake manifold is in place, inspect to make sure seals are in place.
5. Make sure the injector holes are clean and all plugs have been removed.
6. Lube injector O-ring with a drop of clean engine oil to ease installation.
7. Put the tip of each injector into their ports. Push the assembly into place until the injectors are seated in the ports.
8. Install the fuel rail attaching bolts and torque to 22 Nm (200 in. lbs.)
9. Install fuel tube retaining bracket screw and torque to 4 Nm (35 in. lbs.)
10. Connect cam sensor and coolant temperature sensor.
11. Remove covering on lower intake manifold and clean surface.
12. Position the new intake manifold gasket on lower manifold. Install upper manifold into place and tighten bolts and nuts only finger tight, at this time.
NOTE: At no time should the studs be replaced with a bolt and washer.
13. Install the generator bracket to intake manifold bolt and the cylinder head to intake manifold strut bolts. (Do not torque.)
14. Torque intake manifold bolts to 28 Nm (250 in. lbs.) following torque sequence in.
15. Torque generator bracket to intake manifold bolt to 54 Nm (40 ft. lbs.).
16. Torque the cylinder head to intake manifold strut bolts to 54 Nm (40 ft. lbs.)
17. Connect ground strap and MAP sensor electrical connector.
18. Connect vacuum harness to intake plenum.
19. Using a new gasket, connect the EGR tube flange to the intake manifold and torque to 22 Nm (200 in. lbs.).
20. Clip wiring harness into the hole in the throttle cable bracket.
21. Connect the wiring connectors to the throttle position sensor (TPS) and Automatic Idle Speed (AIS) motor.
22. Connect vacuum harness to throttle body.
23. Install the direct ignition system (DIS) coils. Torque fasteners to 12 Nm (105 in. lbs.) (Fig. 45).
24. Lubricate the end of the chassis fuel tube with 30 WT. oil. Connect fuel supply hose to chassis fuel tube assembly. Pull back on the quick connect fitting to ensure complete insertion (Fig. 44).
25. Install throttle cable. .
26. Connect fuel injector
27. Install air cleaner and hose assembly.
28. Connect negative battery
29. If drained, fill cooling system. Refer to Cooling System for procedure.
30. With the DRB Scan Tool use ASD Fuel System Test to pressurize system to check for leaks.